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Search indexed NASA NTRS and DOE OSTI research on propulsion, heat transfer, battery materials and energy systems. Follow report and document links to the original sources.

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At least 73 records · Page 4
All sourcesNASA NTRSDOE OSTI
DOE OSTI2022

Assessment of human nuclear and mitochondrial DNA qPCR assays for quantification accuracy utilizing NIST SRM 2372a

In forensic DNA casework, a highly accurate real-time quantitative polymerase chain reaction (qPCR) assay is recommended per the Scientific Working Group on DNA Analysis Methods (SWGDAM) (SWGDAM Validation Guidelines for DNA Analysis Methods [1]) to determine whether a DNA sample is of sufficient quantity and robust quality to move forward with downstream short tandem repeats (STR) or sequencing analyses. Most of these assays rely on a standard curve, referred to herein and traditionally as absolute qPCR, in which an unknown is compared, relative to that curve. However, one fundamental issue with absolute qPCR is the quantifiable concentration of commercial assay standards can vary depending on (1) origin, i.e., whether from a cell line or a human subject, (2) supplier, (3) lot number, (4) shipping method, etc. In 2018, the National Institute for Standards and Technology (NIST) released a human DNA standard reference material for evaluating qPCR quantification standards, Standard Reference Material (SRM) 2372a, Romsos et al. (2018) [2] which contains three well-characterized human genomic DNA samples: Component A) a single male1 donor, Component B) a single female 1 donor, and Component C) a 1:3 male 2 :female 2 donor, each with certification data for nDNA and informational mitochondrial DNA(mtDNA)/nuclear DNA (nDNA) ratio data. The SRM 2372a was used to assess four qPCR assays: (1) Quantifiler Trio (Thermo Fisher Scientific, Waltham, MA) for nDNA quantification, (2) NovaQUANT (EMD Millipore Corporation, San Diego, CA) for nDNA and mtDNA quantification, (3) a custom duplex mtDNA assay, and (4) a custom triplex mtDNA assay. Additionally, extracts from eighteen (18) skeletal remains were tested with the latter three assays for concordance of DNA concentration and with assays (2) and (3), for the degradation state. Our assessment revealed that an accurate, efficient, and reproducible qPCR assay is dependent on (1) the quality and reliability of the DNA standard, (2) the qPCR chemistry, and (3) the specific primers, and probes (if applicable), used in an assay. Finally, our findings indicate qPCR assays may not always quantify as expected and that performance of each lot should be verified using a well-characterized DNA standard such as the NIST SRM 2372a and adjusted if warranted.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2020

Investigating the Atmospheric Sources and Sinks of Perfluorooctanoic Acid Using a Global Chemistry Transport Model

Perfluorooctanoic acid, PFOA, is one of the many concerning pollutants in our atmosphere; it is highly resistant to environmental degradation processes, which enables it to accumulate biologically. With direct routes of this chemical to the environment decreasing, as a consequence of the industrial phase out of PFOA, it has become more important to accurately model the effects of indirect production routes, such as environmental degradation of precursors; e.g., fluorotelomer alcohols (FTOHs). The study reported here investigates the chemistry, physical loss and transport of PFOA and its precursors, FTOHs, throughout the troposphere using a 3D global chemical transport model, STOCHEM-CRI. Furthermore, this investigation includes an important loss process of PFOA in the atmosphere via the addition of the stabilised Criegee intermediates, hereby referred to as the “Criegee Field.” Whilst reaction with Criegee intermediates is a significant atmospheric loss process of PFOA, it does not result in its permanent removal from the atmosphere. Additionally, the atmospheric fate of the resultant hydroperoxide product from the reaction of PFOA and Criegee intermediates resulted in a ≈0.04 Gg year-1 increase in the production flux of PFOA. Furthermore, the physical loss of the hydroperoxide product from the atmosphere (i.e., deposition), whilst decreasing the atmospheric concentration, is also likely to result in the reformation of PFOA in environmental aqueous phases, such as clouds, precipitation, oceans and lakes. As such, removal facilitated by the “Criegee Field” is likely to simply result in the acceleration of PFOA transfer to the surface (with an expected decrease in PFOA atmospheric lifetime of ≈10 h, on average from ca. 80 h without Criegee loss to 70 h with Criegee loss).

54 ENVIRONMENTAL SCIENCES↗
DOE OSTI2023

Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures

Abstract DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast degradation by nucleases. Recently, we showed how enzymatic polymerization could be harnessed to grow polynucleotide brushes of tunable length and location on the surface of DNA origami nanostructures, which greatly enhances their nuclease stability. Here, we report on strategies that allow for both spatial and temporal control over polymerization through activatable initiation, cleavage, and regeneration of polynucleotide brushes using restriction enzymes. The ability to site‐specifically decorate DNA origami nanostructures with polynucleotide brushes in a spatiotemporally controlled way provides access to “smart” functionalized DNA architectures with potential applications in drug delivery and supramolecular assembly.

Yang, Yunqi↗
DOE OSTI2023

Spatiotemporal Control over Polynucleotide Brush Growth on DNA Origami Nanostructures

DNA nanotechnology provides an approach to create precise, tunable, and biocompatible nanostructures for biomedical applications. However, the stability of these structures is severely compromised in biological milieu due to their fast degradation by nucleases. Recently, we showed how enzymatic polymerization could be harnessed to grow polynucleotide brushes of tunable length and location on the surface of DNA origami nanostructures, which greatly enhances their nuclease stability. Here, in this study, we report on strategies that allow for both spatial and temporal control over polymerization through activatable initiation, cleavage, and regeneration of polynucleotide brushes using restriction enzymes. The ability to site‐specifically decorate DNA origami nanostructures with polynucleotide brushes in a spatiotemporally controlled way provides access to “smart” functionalized DNA architectures with potential applications in drug delivery and supramolecular assembly.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
DOE OSTI2021

Analysis of a new multispecies tumor growth model coupling 3D phase-fields with a 1D vascular network

In this study, we present and analyze a mathematical model for tumor growth incorporating ECM erosion, interstitial flow, and the effect of vascular flow and nutrient transport. The model is of phase-field or diffused-interface type in which multiple phases of cell species and other constituents are separated by smooth evolving interfaces. The model involves a mesoscale version of Darcy’s law to capture the flow mechanism in the tissue matrix. Modeling flow and transport processes in the vasculature supplying the healthy and cancerous tissue, one-dimensional (1D) equations are considered. Since the models governing the transport and flow processes are defined together with cell species models on a three-dimensional (3D) domain, we obtain a 3D–1D coupled model.

3D–1D coupled blood flow models↗
DOE OSTI2023

Dissection of Grass Cell Wall Lignin Formation and their Associated Dirigent Protein

This Final Report describes work underway to establish why monocot (e.g. grasses) lignins are more readily (bio)degradable than their woody gymnosperm, angiosperm, and fern counterparts. Our hypothesis is that monocot specific dirigent protein (DP) sub-families are wholly or partly involved in generating these more readily (bio)degradable lignins. Three approaches are underway: metabolomics and lignin analyses of stem and leaf tissues of the grass, Brachypodium; Crispr/Cas9 gene editing of monocot specific DP sub-families in this species, and recombinant protein expression of Brachypodium’s 44 DPs. Metabolomic and lignin analyses were completed for 6 and 8 week old Brachypodium in order to establish the molecular diversity of its largely phenolic metabolites: Crispr/Cas9 gene editing has also been done on specific DPs known to be expressed in lignifying stems, and T 2 generation plant lines are now being generated, prior to establishing the effects on lignin composition and content; in the recombinant DP work (which addresses establishing the biochemical function of the monocot specific DPs and other DPOs as needed), all 44 constructs have been generated (in collaboration with DOE JGI) and are being systematically expressed in either E. coli or yeast (Pichia sp.) for future studies. Future work will be directed towards bringing the current studies to completion, and in establishing the biochemical basis as to how these more readily (bio)degradable lignins are generated/assembled.

(bio)degradability↗
DOE OSTI2023

Accelerating Adoption of Energy-Efficient Technology with the Thermalize Model

The accelerating impacts of climate change destabilize food systems and ecosystems alongside the communities that rely on them. Thus, climate resilience is a health equity issue at both a physical (relating to biological impacts of pollution and environmental degradation) and a cultural level (loss of subsistence lifestyles, languages, etc). With roughly 20% of US energy-related greenhouse gas emissions stemming from heating, cooling, and powering households, accessible energy-efficient home retrofits are a critical element of climate change mitigation strategies. For communities already producing electricity from renewable sources, like Juneau, incentivizing ductless heat pump upgrades and energy efficiency retrofits provides an accessible pathway to transition households away from oil heating and drastically reduce emissions. Thermalize Juneau is a pilot program that will explore a repeatable framework for accelerating the adoption of energy-efficient technology in Alaska communities. This poster will describe Thermalize Juneau's goals and framework, progress through spring 2021, and future plans.

ductless heat pumps↗
DOE OSTI2021

A Guanidine-Degrading Enzyme Controls Genomic Stability of Ethylene-Producing Cyanobacteria

Recent studies have revealed the prevalence and biological significance of guanidine metabolism in nature. However, the metabolic pathways used by microbes to degrade guanidine or mitigate its toxicity have not been widely studied. Here, via comparative proteomics and subsequent experimental validation, we demonstrate that Sll1077, previously annotated as an agmatinase enzyme in the model cyanobacterium Synechocystis sp. PCC 6803, is more likely a guanidinase as it can break down guanidine rather than agmatine into urea and ammonium. The model cyanobacterium Synechococcus elongatus PCC 7942 strain engineered to express the bacterial ethylene-forming enzyme (EFE) exhibits unstable ethylene production due to toxicity and genomic instability induced by accumulation of the EFE-byproduct guanidine. Co-expression of EFE and Sll1077 significantly enhances genomic stability and enables the resulting strain to achieve sustained high-level ethylene production. These findings expand our knowledge of natural guanidine degradation pathways and demonstrate their biotechnological application to support ethylene bioproduction.

59 BASIC BIOLOGICAL SCIENCES↗
DOE OSTI2021

Composition and Structure of Fluorescent Graphene Quantum Dots Generated by Enzymatic Degradation of Graphene Oxide

The broad applications of carbon nanomaterials (CNMs) in both materials and life sciences necessitate investigation of their metabolites due to the inevitable contact of CNMs and biological systems. Graphene oxide (GO), along with other types of CNMs, can be enzymatically degraded by myeloperoxidase (MPO), an enzyme released during the innate immune response. However, the enzymatic degradation products are neither well-defined nor well-understood. Some products generated during MPO-catalyzed degradation of GO could emit blue photoluminescence (PL) and were simply dubbed graphene quantum dots (GQDs) without further elucidating their structures. In this work, we use liquid chromatography-mass spectrometry (LC-MS) to isolate and elucidate chemical structures of the MPO-catalyzed degradation products. A general chemical formula screening workflow was developed for the GQDs, which are in the form of polyaromatic hydrocarbons (PAHs), obtained in the degradation products. Structures of the PAHs responsible for the blue PL were further proposed using density functional theory (DFT) calculations. Our results indicated that structures with several conjugated benzene rings are likely to generate the observed PL. This work provides insights into the mechanism of enzymatic degradation and open opportunities for fluorescence imaging of GO in biological systems.

composition and structure screening↗
DOE OSTI2023

Substrate-independent expression of key functional genes in Cycloclasticus pugetii strain PS-1 limits their use as markers for PAH biodegradation

Microbial degradation of petroleum hydrocarbons is a crucial process for the clean-up of oil-contaminated environments. Cycloclasticus spp. are well-known polycyclic aromatic hydrocarbon (PAH) degraders that possess PAH-degradation marker genes including rhd3α, rhd2α, and pahE. However, it remains unknown if the expression of these genes can serve as an indicator for active PAH degradation. Here, we determined transcript-to-gene (TtG) ratios with (reverse transcription) qPCR in cultures of Cycloclasticus pugetii strain PS-1 grown with naphthalene, phenanthrene, a mixture of these PAHs, or alternate substrates (i.e., no PAHs). Mean TtG ratios of 1.99 × 10 −2 , 1.80 × 10 −3 , and 3.20 × 10 −3 for rhd3α, rhd2α, and pahE, respectively, were measured in the presence or absence of PAHs. The TtG values suggested that marker-gene expression is independent of PAH degradation. Measurement of TtG ratios in Arctic seawater microcosms amended with water-accommodated crude oil fractions, and incubated under in situ temperature conditions (i.e., 1.5°C), only detected Cycloclasticus spp. rhd2α genes and transcripts (mean TtG ratio of 4.15 × 10 −1 ). The other marker genes—rhd3α and pahE—were not detected, suggesting that not all Cycloclasticus spp. carry these genes and a broader yet-to-be-identified repertoire of PAH-degradation genes exists. The results indicate that the expression of PAH marker genes may not correlate with PAH-degradation activity, and transcription data should be interpreted cautiously.

59 BASIC BIOLOGICAL SCIENCES↗
NASA NTRS2012

Is Water a Universal Solvent for Life?

There are strong reasons to believe that the laws, principles and constraints of physics and chemistry are universal. It is much less clear how this universality translates into our understanding of the origins of life. Conventionally, discussions of this topic focus on chemistry that must be sufficiently rich to seed life. Although this is clearly a prerequisite for the emergence of living systems, I propose to focus instead on self-organization of matter into functional structures capable of reproduction, evolution and responding to environmental changes. In biology, most essential functions are largely mediated by noncovalent interactions (interactions that do not involve making or breaking chemical bonds). Forming chemical bonds is only a small part of what living systems do. There are specific implications of this point of view for universality. I will concentrate on one of these implications. Strength of non-covalent interactions must be properly tuned. If they were too weak, the system would exhibit undesired, uncontrolled response to natural fluctuations of physical and chemical parameters. If they were too strong kinetics of biological processes would be slow and energetics costly. This balance, however, is not a natural property of complex chemical systems. Instead, it has to be achieved with the aid of an appropriate solvent for life. In particular, potential solvents for life must be characterized by a high dielectric constant to ensure solubility of polar species and sufficient flexibility of biological structures stabilized by electrostatic interactions. Among these solvents, water exhibits a remarkable trait that it also promotes solvophobic (hydrophobic) interactions between non-polar species, typically manifested by a tendency of these species to aggregate and minimize their contacts with the aqueous solvent. Hydrophobic interactions are responsible, at least in part, for many self-organization phenomena in biological systems, such as the formation of cellular boundary structures or protein folding. Strengths of electrostatic and hydrophobic interactions are similar and can be balanced over a wide range of temperatures, which considerably increases the repertoire of interactions that can be used to modulate biological functions. Some properties of water, e.g. its chemical activity against polymerization reactions, are considered as unfavorable to life. In actuality, this might be a favorable trait because life requires a balance between constructive and destructive processes. For example, molecules synthesized in response to specific conditions must be degraded once these conditions change. Otherwise regulation of biological processes would be virtually impossible. Water might not be the only liquid with favorable properties for supporting life. It has been proposed that formamide, which might be present elsewhere in the universe in sufficient quantities to warrant interest, could be a potential alternative to water for the origin of life. However, this will remain highly hypothetical until it is demonstrated in further studies on its physical, chemical and biological properties it is capable of mediating self-organization of matter and providing proper balance between different types of non-covalent interactions.

Pohorill, Andrew↗
NASA NTRSDate not supplied

Microbial Pigments and Their Degradation Products as Biosignatures

Carotenoids are a class of vibrant biological pigments that have a characteristic chemical structure centered around a polyene core (Lu et al. 2018). Carotenoids and their derivatives are candidate biosignatures because they can persist in the terrestrial geologic record for up to 1.73 billion years (Vinnichenko et al. 2020), have specific structures that are likely the result of complex pathways, mediate the survival of many microorganisms in Mars and Ocean Worlds analog environments, and are detectable with multiple techniques, including Raman spectroscopy. In this project, we aim to investigate the detectability of carotenoid pigments with different spectroscopic methods to inform future instrument selection. We compare the spectra of five unaltered carotenoids, two model compounds, and carotenoid-forming archaeon with visible and deep UV Raman spectroscopy and UVVis absorption spectrophotometry. We then use one model pigment, beta-carotene, to evaluate the likelihood that unique spectral properties of carotenoids, or their refractory byproducts, would be preserved and detectable on a remote planetary surface by exposing it to simulated conditions for Mars. Sample Acquisition. Pigments betacarotene, lutein, zeaxanthin, astaxanthin, and lycopene were purchased from Sigma Aldrich. Halobacterium salinarum NRC-1 was acquired from Carlina Biological and grown in Halobacterium media. Mineral salts including sodium sulfate, sodium carbonate, and halite were used to form matrices in which the beta-carotene was embedded before exposure. Pigment-mineral mixes were at a 1:10 ratio in water. Analytical Techniques. Deep UV Raman data were collected on a custom laboratory mapping spectrometer called MOBIUS (Mineral and Organic Based Investigations using Ultraviolet Spectroscopy), which is an analog to the SHERLOC instrument on the Mars 2020 Perseverance rover (Bhartia et al. 2021). It features a 248.56 nm NeCu pulsed laser, liquid nitrogen-cooled detector, and tunable optical setup. Visible Raman data were collected using a Horiba Jobin Yvon LabRam HR spectrometer with a frequencydoubled Nd:YAG laser (532 nm) and a HeNe laser (633 nm). A VWR 6300 PC UV/Visible Spectrophotometer was used to collect absorption data for carotenoid solutions, model compounds, and solvents in UVpermissible capped cuvettes. Data were collected from 190-1100 nm at 1 nm increments. All spectral data were analyzed using Igor Pro 9 (Wavemetrics). Irradiation. We used a vacuum chamber equipped with a cryostat and a flood electron gun to simulate Martian surface temperatures, low pressures, and ionizing radiation (10keV, 10μA for 6h at 200K for our initial tests). The samples were prepared by drying the pigment-mineral mix onto polished metal tabs, then mounted on the cryostat for processing. Samples were then analyzed directly on the tabs after exposure. Results: In comparing the visible and deep UV Raman spectra of unaltered pigments, we found that they differed drastically. Carotenoids are often studied with visible Raman and typically have peaks at 1525 cm-1 and 1157 cm-1, due to the stretching of the C=C and C-C bonds in the polyene structure. However, in deep UV, the strongest feature is at ~1630 cm-1 and is broad, possibly indicating that multiple peaks are forming this feature. This stark difference is likely due to different preresonant enhancement effects. The UV-Vis results show that there is an absorption band in the deep UV <300 nm, which supports the hypothesis that the 248.6 nm excitation is interrogating another aspect of carotenoids than visible Raman. Our preliminary exposure tests indicated that pigments – even without minerals present - were largely unaltered in the applied conditions, with only a slight broadening in the primary polyene peaks apparent in the visible Raman data. Figure 1. A) Visible vs. deep UV Raman spectra of unaltered beta carotene. B) Schematic of exposure. Conclusions: Our results to date indicate that deep UV and visible Raman spectroscopy, both techniques with planetary mission heritage from Mars 2020 (Wiens et al. 2021, Bhartia et al. 2021), may be used in a complementary manner to observe carotenoids. In addition, we find that beta-carotene is largely resistant to our current exposure conditions, though there may be some amount of amorphization of the material which could cause the broadening of the peaks at 1525 and 1157 cm-1. As a next step, we aim to increase the dosage and duration of exposure to observe degradation of the parent pigment, possibly add UV as a factor via an Ar mini-arc UV lamp and use GC-MS to characterize possible degradation products.

pigments↗
DOE OSTI2020

Energetic Control of Redox-Active Polymers toward Safe Organic Bioelectronic Materials

Avoiding faradaic side reactions during the operation of electrochemical devices is important to enhance the device stability, to achieve low power consumption, and to prevent the formation of reactive side-products. This is particularly important for bioelectronic devices, which are designed to operate in biological systems. While redox-active materials based on conducting and semiconducting polymers represent an exciting class of materials for bioelectronic devices, they are susceptible to electrochemical side-reactions with molecular oxygen during device operation. In this work, electrochemical side reactions with molecular oxygen are shown to occur during organic electrochemical transistor (OECT) operation using high-performance, state-of-the-art OECT materials. Depending on the choice of the active material, such reactions yield hydrogen peroxide (H 2 O 2 ), a reactive side-product, which may be harmful to the local biological environment and may also accelerate device degradation. A design strategy is reported for the development of redox-active organic semiconductors based on donor–acceptor copolymers that prevents the formation of H 2 O 2 during device operation. This study elucidates the previously overlooked side-reactions between redox-active conjugated polymers and molecular oxygen in electrochemical devices for bioelectronics, which is critical for the operation of electrolyte-gated devices in application-relevant environments.

36 MATERIALS SCIENCE↗
DOE OSTI2025

Vibrational sum frequency generation spectroscopy reveals the inertness of chromium oxide (001) surfaces

Nanoengineered metal oxides such as Cr(III)-oxide (chromia) films have diverse potential applications in corrosion inhibition, remediation, energy generation, catalysis, data storage, and biological and environmental systems. Concerns about material degradation or oxidation to toxic chromate necessitate an understanding of chromia/aqueous interfaces, beginning with their hydroxylation and hydration behavior. Vibrational sum-frequency generation spectroscopy (vSFG) provides specific molecular-level information about water at the oxide/aqueous junction with high surface selectivity. To overcome the strong absorber problem typical of certain metal oxides in the UV–visible range during nonlinear optical studies, we employed molecular beam epitaxy to deposit transparent, epitaxial nanofilms of Cr 2 O 3 with (001) crystalline orientation on sapphire (Al 2 O 3 (001)) substrates, as confirmed by atomic force microscopy and X-ray diffraction. vSFG spectra of the air and water interfaces of the Cr 2 O 3 (001) films reveal hydroxyl features corresponding to both dissociated and molecular water on the surface. In contrast to the dangling hydroxyls found on the bare Al 2 O 3 (001) substrate, the hydroxyl groups on the deposited Cr 2 O 3 (001) nanofilm do not readily undergo isotopic H/D exchange when exposed to varying forms of D 2 O under ambient conditions. When considering the chemistries of the corresponding trivalent cations in aqueous solution, the finding is at variance with their similar acidities and proton exchange dynamics but consistent with markedly slower inner-sphere water ligand exchange of hexaquo Cr 3+ . This finding challenges the idea that proton and water exchange at the water/Cr₂O₃(001) interface are solely correlated, driven by the strength of metal-bridging oxygen bonds and surface hydroxyl distribution, without direct causation.

Boamah-Agyemang, Mavis D. [Pacific Northwest Natio↗
NASA NTRS1999

Marching Microbes

Under an SBIR contract with Marshall Space Flight Center, Micro-Bac International developed a new system for the treatment of wastewater based on the metabolic activity of photorphic bacteria. These microorganisms are now being sold as a liquid product called Mega-Bac TF. It is currently used for septic systems and wastewater ponds, lakes and lagoons to degrade fat, oil, fecal matter and other biologically derived wastes. Potential applications include homes, agriculture, food processors and chemical manufacturing.

Source record↗